Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2 Emergence Amidst Community-Acquired Respiratory Viruses

• Published in: The Journal of infectious diseases 2020-09, Vol.222 (8), p.1270-1279
• Main Authors: Leuzinger, Karoline, Roloff, Tim, Gosert, Rainer, Sogaard, Kirstin, Naegele, Klaudia, Rentsch, Katharina, Bingisser, Roland, Nickel, Christian H, Pargger, Hans, Bassetti, Stefano, Bielicki, Julia, Khanna, Nina, Tschudin Sutter, Sarah, Widmer, Andreas, Hinic, Vladimira, Battegay, Manuel, Egli, Adrian, Hirsch, Hans H
• Format: Article
• Language: English
• Subjects: Adolescent; Adult; Aged; Aged, 80 and over; Betacoronavirus - genetics; Betacoronavirus - isolation & purification; Child; Child, Preschool; Children; Clinical Laboratory Techniques; Coinfection - epidemiology; Coinfection - immunology; Coinfection - virology; Communicable Diseases, Emerging - epidemiology; Communicable Diseases, Emerging - virology; Coronaviridae; Coronavirus Envelope Proteins; Coronavirus Infections - diagnosis; Coronavirus Infections - epidemiology; Coronavirus Infections - virology; Coronavirus Nucleocapsid Proteins; Coronaviruses; COVID-19; COVID-19 Testing; Epidemiology; Female; Humans; Immunological memory; Infant; Infant, Newborn; Influenza; Major; Male; Middle Aged; Nucleocapsid Proteins - genetics; Pandemics; Phosphoproteins; Pneumonia, Viral - diagnosis; Pneumonia, Viral - epidemiology; Pneumonia, Viral - virology; Respiratory syncytial virus; Respiratory Tract Infections - epidemiology; Respiratory Tract Infections - virology; Rhinovirus; SARS-CoV-2; Severe acute respiratory syndrome coronavirus 2; Spike Glycoprotein, Coronavirus - genetics; Viral Envelope Proteins; Viruses; World Health Organization; Young Adult
• ISSN: 0022-1899; 1537-6613
• DOI: 10.1093/infdis/jiaa464

Abstract Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in China as the cause of coronavirus disease 2019 in December 2019 and reached Europe by late January 2020, when community-acquired respiratory viruses (CARVs) are at their annual peak. We validated the World Health Organization (WHO)–recommended SARS-CoV-2 assay and analyzed the epidemiology of SARS-CoV-2 and CARVs. Methods Nasopharyngeal/oropharyngeal swabs (NOPS) from 7663 patients were prospectively tested by the Basel S-gene and WHO-based E-gene (Roche) assays in parallel using the Basel N-gene assay for confirmation. CARVs were prospectively tested in 2394 NOPS by multiplex nucleic acid testing, including 1816 (75%) simultaneously for SARS-CoV-2. Results The Basel S-gene and Roche E-gene assays were concordant in 7475 cases (97.5%) including 825 (11%) SARS-CoV-2 positives. In 188 (2.5%) discordant cases, SARS-CoV-2 loads were significantly lower than in concordant positive ones and confirmed in 105 (1.4%). Adults were more frequently SARS-CoV-2 positive, whereas children tested more frequently CARV positive. CARV coinfections with SARS-CoV-2 occurred in 1.8%. SARS-CoV-2 replaced CARVs within 3 weeks, reaching 48% of all detected respiratory viruses followed by rhinovirus/enterovirus (13%), influenza virus (12%), coronavirus (9%), respiratory syncytial virus (6%), and metapneumovirus (6%). Conclusions Winter CARVs were dominant during the early SARS-CoV-2 pandemic, impacting infection control and treatment decisions, but were rapidly replaced, suggesting competitive infection. We hypothesize that preexisting immune memory and innate immune interference contribute to the different SARS-CoV-2 epidemiology among adults and children. Community-acquired respiratory viruses were dominant during the early severe acute respiratory syndrome coronavirus 2 pandemic in winter 2020, but were rapidly replaced, suggesting competitive infection. Preexisting immune memory and innate immune interference may contribute to the different epidemiology among adults and children.